X-745534-G-A

Variant names:

• chrX-745534-G-A
• rs1468111

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0316 in 152,206 control chromosomes in the GnomAD database, including 95 homozygotes. There are 2,251 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.032 (95 hom., 2251 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0316 (4810/152206) while in subpopulation AFR AF = 0.0451 (1874/41524). AF 95% confidence interval is 0.0434. There are 95 homozygotes in GnomAd4. There are 2251 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4806 AN: 152088 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0316 AC: 4810 AN: 152206 Hom.: 95 Cov.: 32 AF XY: 0.0303 AC XY: 2251 AN XY: 74406

African (AFR) AF: 0.0451 AC: 1874 AN: 41524

American (AMR) AF: 0.0271 AC: 415 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00747 AC: 36 AN: 4818

European-Finnish (FIN) AF: 0.0218 AC: 231 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2079 AN: 68014

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Bravo AF: 0.0326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1468111; hg19: chrX-706269;